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Nucleic Acids Research  
Volume 50 Issue 11
 
24 June 2022
 
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NAR Breakthrough Article
 
 
 
Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor border= 
 
Prajwal Karki; Travis D Carney; Cristina Maracci ; Andriy S Yatsenko; Halyna R Shcherbata ...
 
 
 
Critical Reviews and Perspectives
 
 
 
Considerations and recommendations for assessment of plasma protein binding and drug'drug interactions for siRNA therapeutics border= 
 
Sara C Humphreys; John A Davis; Sajida Iqbal ; Amin Kamel; Kenneth Kulmatycki ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA border= 
 
Stefan Mair; Kevin Erharter; Eva Renard ; Karl Brillet; Melanie Brunner ...
 
 
 
Computational Biology
 
 
 
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models border= 
 
João Capela ; Davide Lagoa; Ruben Rodrigues; Emanuel Cunha; Fernando Cruz ...
 
 
The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets border= 
 
Gabrielle Deschamps-Francoeur; Sonia Couture; Sherif Abou-Elela ; Michelle S Scott
 
 
 
 
 
Data Resources and Analyses
 
 
 
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions border= 
 
Mario Rodríguez Mestre; Linyi Alex Gao; Shiraz A Shah ; Adrián López-Beltrán; Alejandro González-Delgado ...
 
 
HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock border= 
 
Samu V Himanen; Mikael C Puustinen; Alejandro J Da Silva ; Anniina Vihervaara; Lea Sistonen
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Phosphorylation-dependent association of human chromatin protein PC4 to linker histone H1 regulates genome organization and transcription border= 
 
Pallabi Mustafi; Mingli Hu; Sujata Kumari ; Chandrima Das; Guohong Li ...
 
 
Schlafen 5 suppresses human immunodeficiency virus type 1 transcription by commandeering cellular epigenetic machinery border= 
 
Jiwei Ding; Shujie Wang; Zhen Wang ; Shumin Chen; Jianyuan Zhao ...
 
 
TBX2 acts as a potent transcriptional silencer of tumour suppressor genes through interaction with the CoREST complex to sustain the proliferation of breast cancers border= 
 
Alexander J McIntyre; Charlotte Z Angel; James S Smith ; Amy Templeman; Katherine Beattie ...
 
 
 
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp border= 
 
Hiraku Takada; Zachary F Mandell; Helen Yakhnin ; Anastasiya Glazyrina; Shinobu Chiba ...
 
 
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress border= 
 
Qin Gu; Yujie Wang; Xiaozhen Zhao ; Bingqin Yuan; Mengxuan Zhang ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination border= 
 
Delyana P Vasileva; Jared C Streich; Leah H Burdick ; Dawn M Klingeman; Hari B Chhetri ...
 
 
MutL binds to 3 resected DNA ends and blocks DNA polymerase access border= 
 
Alessandro Borsellini; Joyce H G Lebbink; Meindert H Lamers
 
 
THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1 border= 
 
Juliette A Kamp; Bennie B L G Lemmens; Ron J Romeijn ; Román González-Prieto; Jesper V Olsen ...
 
 
Noncanonical NF-kappa B factor p100/p52 regulates homologous recombination and modulates sensitivity to DNA-damaging therapy border= 
 
Brian Budke; Alison Zhong; Katherine Sullivan ; Chanyoung Park; David I Gittin ...
 
 
Insight into RNA'DNA primer length counting by human primosome border= 
 
Andrey G Baranovskiy; Alisa E Lisova; Lucia M Morstadt; Nigar D Babayeva ; Tahir H Tahirov
 
 
 
Molecular Biology
 
 
 
Vectorial folding of telomere overhang promotes higher accessibility border= 
 
Tapas Paul; Patricia L Opresko; Taekjip Ha; Sua Myong
 
 
Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution border= 
 
Marie-Line Bortolin-Cavaillé; Aurélie Quillien; Supuni Thalalla Gamage ; Justin M Thomas; Aldema Sas-Chen ...
 
 
40S hnRNP particles are a novel class of nuclear biomolecular condensates border= 
 
Michal Domanski; Emil Dedic; Maria Escura Pérez; Antoine Cléry ; Sébastien Campagne ...
 
 
KDM6B promotes PARthanatos via suppression of O6-methylguanine DNA methyltransferase repair and sustained checkpoint response border= 
 
Mingming Yang; Chenliang Wang; Mi Zhou ; Lei Bao; Yanan Wang ...
 
 
Topoisomerase 1 inhibits MYC promoter activity by inducing G-quadruplex formation border= 
 
Josephine Geertsen Keller; Kirstine Mejlstrup Hymøller; Maria Eriksen Thorsager ; Noriko Y Hansen; Jens Uldum Erlandsen ...
 
 
ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia border= 
 
Linjiang Lao; Isabelle Bourdeau; Lucia Gagliardi ; Xiao He; Wei Shi ...
 
 
 
Nucleic Acid Enzymes
 
 
 
The Xer activation factor of TLCΦ expands the possibilities for Xer recombination border= 
 
Solange Miele; James Iain Provan; Justine Vergne ; Christophe Possoz; Françoise Ochsenbein ...
 
 
Allosteric couplings upon binding of RfaH to transcription elongation complexes border= 
 
José Alejandro Molina; Pablo Galaz-Davison; Elizabeth A Komives; Irina Artsimovitch ; César A Ramírez-Sarmiento
 
 
Noncanonical prokaryotic X family DNA polymerases lack polymerase activity and act as exonucleases border= 
 
Maria Prostova; Evgeniy Shilkin; Alexandra A Kulikova ; Alena Makarova; Sergei Ryazansky ...
 
 
CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity border= 
 
Nicole D Marino; Rafael Pinilla-Redondo; Joseph Bondy-Denomy
 
 
Bi-PE: bi-directional priming improves CRISPR/Cas9 prime editing in mammalian cells border= 
 
Rui Tao; Yanhong Wang; Yaoge Jiao ; Yun Hu; Li Li ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli border= 
 
Linda Popella; Jakob Jung; Phuong Thao Do ; Regan J Hayward; Lars Barquist ...
 
 
Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation border= 
 
Jelena Micic; Olga Rodríguez-Galán; Reyes Babiano ; Fiona Fitzgerald; José Fernández-Fernández ...
 
 
HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript 
 
Tam Vo; Tayvia Brownmiller; Katherine Hall; Tamara L Jones ; Sulbha Choudhari ...
 
 
The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects border= 
 
Linda Krause; Florian Willing; Alexandra Zoi Andreou ; Dagmar Klostermeier
 
 
Allosteric regulation of noncoding RNA function by microRNAs border= 
 
Carlos Gorbea; Abdalla Elhakiem; Demián Cazalla
 
 
 
Structural Biology
 
 
 
Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila border= 
 
Evgeniya Tikhonova; Sofia Mariasina; Sergey Efimov ; Vladimir Polshakov; Oksana Maksimenko ...
 
 
Role of aIF5B in archaeal translation initiation border= 
 
Ramy Kazan; Gabrielle Bourgeois; Christine Lazennec-Schurdevin; Eric Larquet ; Yves Mechulam ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue border= 
 
Migl- Tomkuvien-; Markus Meier; Diana Ikasalait- ; Julia Wildenauer; Visvaldas Kairys ...
 
 
Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor border= 
 
Katja Leben; Žiga Strmšek; Tina Lebar ; Anže Verbič; Matej Dragovan ...
 
 
An in-library ligation strategy and its application in CRISPR/Cas9 screening of high-order gRNA combinations border= 
 
Zhike Lu; Ke Ni; Yingying Wang ; Yangfan Zhou; Yini Li ...
 
 
A pathway independent multi-modular ordered control system based on thermosensors and CRISPRi improves bioproduction in Bacillus subtilis border= 
 
Wenwen Yu; Ke Jin; Yaokang Wu ; Quanwei Zhang; Yanfeng Liu ...
 
 
 
Methods Online
 
 
 
ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats border= 
 
Lukas Frank; Anne Rademacher; Norbert Mücke ; Stephan M Tirier; Emma Koeleman ...
 
 
Ligation-assisted homologous recombination enables precise genome editing by deploying both MMEJ and HDR border= 
 
Zhihan Zhao; Peng Shang; Fanny Sage ; Niels Geijsen
 
 
Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing border= 
 
Heleen Masset; Jia Ding; Eftychia Dimitriadou ; Sophie Debrock; Olga Tšuiko ...
 
 
TransposonUltimate: software for transposon classification, annotation and detection border= 
 
Kevin Riehl; Cristian Riccio; Eric A Miska ; Martin Hemberg
 
 
CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells border= 
 
Yuxi Ai; Dongming Liang; Jeremy E Wilusz
 
 
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming border= 
 
Ran Zhou; Xia Xiao; Ping He; Yuancun Zhao; Mengying Xu ...
 
 
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